title: VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts.
abstract: Creation of a vast variety of proteins is accomplished by genetic variation and a variety of alternative splicing transcripts. Currently, however, the abundant available data on genetic variation and the transcriptome are stored independently and in a dispersed fashion. In order to provide a research resource regarding the effects of human genetic polymorphism on various transcripts, we developed VarySysDB, a genetic polymorphism database based on 187,156 extensively annotated matured mRNA transcripts from 36,073 loci provided by H-InvDB. VarySysDB offers information encompassing published human genetic polymorphisms for each of these transcripts separately. This allows comparisons of effects derived from a polymorphism on different transcripts. The published information we analyzed includes single nucleotide polymorphisms and deletion-insertion polymorphisms from dbSNP, copy number variations from Database of Genomic Variants, short tandem repeats and single amino acid repeats from H-InvDB and linkage disequilibrium regions from D-HaploDB. The information can be searched and retrieved by features, functions and effects of polymorphisms, as well as by keywords. VarySysDB combines two kinds of viewers, GBrowse and Sequence View, to facilitate understanding of the positional relationship among polymorphisms, genome, transcripts, loci and functional domains. We expect that VarySysDB will yield useful information on polymorphisms affecting gene expression and phenotypes. VarySysDB is available at http://h-invitational.jp/varygene/.
authors.affiliation: Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Japan Biological Informatics Consortium, Hitachi Software Engineering Co., Ltd., Tokyo, Japan.
authors.forename: Makoto K
authors.initials: MK
authors.lastname: Shimada
authors.forename: Ryuzou
authors.initials: R
authors.lastname: Matsumoto
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Hayakawa
authors.forename: Ryoko
authors.initials: R
authors.lastname: Sanbonmatsu
authors.forename: Craig
authors.initials: C
authors.lastname: Gough
authors.forename: Yumi
authors.initials: Y
authors.lastname: Yamaguchi-Kabata
authors.forename: Chisato
authors.initials: C
authors.lastname: Yamasaki
authors.forename: Tadashi
authors.initials: T
authors.lastname: Imanishi
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
mesh_terms: D017398:Alternative Splicing; D030561:Databases, Nucleic Acid; D006801:Humans; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000737:chemistry*; D012091:Repetitive Sequences, Nucleic Acid; D014584:User-Computer Interface
chemical_list: D012333:RNA, Messenger